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Volumn 10, Issue 6, 2011, Pages

Gapped spectral dictionaries and their applications for database searches of tandem mass spectra

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; TANDEM MASS SPECTROMETRY; CELL STRAIN HEK293; CHEMISTRY; HUMAN; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS; SHEWANELLA;

EID: 79958012078     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.002220     Document Type: Article
Times cited : (20)

References (33)
  • 2
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: De novo peptide sequencing via probabilistic network modeling
    • DOI 10.1021/ac048788h
    • Frank, A., and Pevzner, P. (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 77, 964-973 (Pubitemid 40261761)
    • (2005) Analytical Chemistry , vol.77 , Issue.4 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 3
    • 66749129629 scopus 로고    scopus 로고
    • A ranking-based Scoring Function for peptide-spectrum matches
    • Frank, A. (2009) A ranking-based Scoring Function for peptide-spectrum matches. J. Proteome Res., 8, 2241-2252
    • (2009) J. Proteome Res. , vol.8 , pp. 2241-2252
    • Frank, A.1
  • 4
    • 59149096107 scopus 로고    scopus 로고
    • Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra
    • Kim, S., Gupta, N., Bandeira, N., and Pevzner, P. A. (2009) Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol. Cell. Proteomics 8, 53-69
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 53-69
    • Kim, S.1    Gupta, N.2    Bandeira, N.3    Pevzner, P.A.4
  • 5
    • 67650535647 scopus 로고    scopus 로고
    • Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification
    • Kim, S., Bandeira, N., and Pevzner, P. A. (2009) Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification. Mol. Cell. Proteomics 8, 1391-1400
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 1391-1400
    • Kim, S.1    Bandeira, N.2    Pevzner, P.A.3
  • 6
    • 17444406699 scopus 로고    scopus 로고
    • Identification of protein modifications using MS/MS de novo sequencing and the opensea alignment algorithm
    • Searle, B. C., Dasari, S., Wilmarth, P. A., Turner, M., Reddy, A. P., David, L. L., and Nagalla, S. R. (2005) Identification of protein modifications using MS/MS de novo sequencing and the opensea alignment algorithm. J. Proteome Res. 4, 546-554
    • (2005) J. Proteome Res. , vol.4 , pp. 546-554
    • Searle, B.C.1    Dasari, S.2    Wilmarth, P.A.3    Turner, M.4    Reddy, A.P.5    David, L.L.6    Nagalla, S.R.7
  • 7
    • 0036828610 scopus 로고    scopus 로고
    • Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry
    • Johnson, R. S., and Taylor, J. A. (2002) Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol. Biotechnol. 22, 301-315
    • (2002) Mol. Biotechnol. , vol.22 , pp. 301-315
    • Johnson, R.S.1    Taylor, J.A.2
  • 8
    • 0035958869 scopus 로고    scopus 로고
    • Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches
    • Huang, L., Jacob, R. J., Pegg, S. C., Baldwin, M. A., Wang, C. C., Burlingame, A. L., and Babbitt, P. C. (2001) Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches. J. Biol. Chem. 276, 28327-28339
    • (2001) J. Biol. Chem. , vol.276 , pp. 28327-28339
    • Huang, L.1    Jacob, R.J.2    Pegg, S.C.3    Baldwin, M.A.4    Wang, C.C.5    Burlingame, A.L.6    Babbitt, P.C.7
  • 9
    • 0028575316 scopus 로고
    • Error-tolerant identification of peptides in sequence databases by peptide sequence tags
    • Mann, M., and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390-4399 (Pubitemid 124006101)
    • (1994) Analytical Chemistry , vol.66 , Issue.24 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 10
    • 0029645432 scopus 로고
    • Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
    • Yates, J. R., 3rd, Eng, J. K., and McCormack, A. L. (1995) Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202-3210
    • (1995) Anal. Chem. , vol.67 , pp. 3202-3210
    • Yates III, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 11
    • 0035350894 scopus 로고    scopus 로고
    • Mass spectrometry allows direct identification of proteins in large genomes
    • Küster, B., Mortensen, P., Andersen, J. S., and Mann, M. (2001) Mass spectrometry allows direct identification of proteins in large genomes. Proteomics. 1, 641-650 (Pubitemid 33588315)
    • (2001) Proteomics , vol.1 , Issue.5 , pp. 641-650
    • Kuster, B.1    Mortensen, P.2    Andersen, J.S.3    Mann, M.4
  • 12
    • 0035346719 scopus 로고    scopus 로고
    • Interrogating the human genome using uninterpreted mass spectrometry data
    • Choudhary, J. S., Blackstock, W. P., and Creasy, D. M., Cottrell, J. S. (2001) Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics. 1, 651-667
    • (2001) Proteomics , vol.1 , pp. 651-667
    • Choudhary, J.S.1    Blackstock, W.P.2    Creasy, D.M.3    Cottrell, J.S.4
  • 14
    • 33846884410 scopus 로고    scopus 로고
    • Improving gene annotation using peptide mass spectrometry
    • DOI 10.1101/gr.5646507
    • Tanner, S., Shen, Z., Ng, J., Florea, L., Guigó, R., Briggs, S. P., and Bafna, V. (2007) Improving gene annotation using peptide mass spectrometry. Genome Res. 17, 231-239 (Pubitemid 46220768)
    • (2007) Genome Research , vol.17 , Issue.2 , pp. 231-239
    • Tanner, S.1    Shen, Z.2    Ng, J.3    Florea, L.4    Guigo, R.5    Briggs, S.P.6    Bafna, V.7
  • 16
    • 77952980794 scopus 로고    scopus 로고
    • Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
    • doi: 10.1101/gr. 103119.109
    • Borchert, N., Dieterich, C., Krug, K., Schutz, W., Jung, S., Nordheim, A., Sommer, R. J., and Macek, B. (2010) Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Research, doi: 10.1101/gr. 103119.109
    • (2010) Genome Research
    • Borchert, N.1    Dieterich, C.2    Krug, K.3    Schutz, W.4    Jung, S.5    Nordheim, A.6    Sommer, R.J.7    Macek, B.8
  • 18
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • DOI 10.1021/ac050102d
    • Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639 (Pubitemid 41542287)
    • (2005) Analytical Chemistry , vol.77 , Issue.14 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 20
    • 0032108018 scopus 로고    scopus 로고
    • Finding the k shortest paths
    • Eppstein, D. (1999) Finding the k shortest paths. SIAM J. Comput. 28, 652-673
    • (1999) SIAM J. Comput. , vol.28 , pp. 652-673
    • Eppstein, D.1
  • 21
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: A strike against decoy databases
    • Kim, S., Gupta, N., and Pevzner, P. A. (2008) Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 7, 3354-3363
    • (2008) J. Proteome Res. , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 25
  • 26
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J., McCormack, A., and Yates, J. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 7, 655-667
    • (1994) J. Am. Soc. Mass Spectrom. , vol.7 , pp. 655-667
    • Eng, J.1    McCormack, A.2    Yates, J.3
  • 27
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • DOI 10.1021/ac025747h
    • Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (Pubitemid 35215372)
    • (2002) Analytical Chemistry , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 29
    • 70349912263 scopus 로고    scopus 로고
    • False discovery rates of protein identifications: A strike against the two-peptide rule
    • Gupta, N., and Pevzner, P. (2009) False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res. 8 4173-4181
    • (2009) J Proteome Res. , vol.8 , pp. 4173-4181
    • Gupta, N.1    Pevzner, P.2
  • 31
    • 33847234661 scopus 로고    scopus 로고
    • Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry
    • Bern, M., Cai, Y., and Goldberg, D. (2007) Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry. Anal. Chem. 79, 1393-1400
    • (2007) Anal. Chem. , vol.79 , pp. 1393-1400
    • Bern, M.1    Cai, Y.2    Goldberg, D.3
  • 32
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • DOI 10.1038/nmeth1019, PII NMETH1019
    • Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods 4, 207-214 (Pubitemid 46358868)
    • (2007) Nature Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.